Variant report

Variant	rs1871500
Chromosome Location	chr15:59949890-59949891
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59949269-59949936	Hela-S3	cervix:	n/a	n/a
2	NR2C2	chr15:59949283-59949946	Hela-S3	cervix:	n/a	n/a
3	MYC	chr15:59949173-59949998	K562	blood:	n/a	n/a
4	GABPA	chr15:59949269-59950307	K562	blood:	n/a	n/a
5	TAF1	chr15:59949269-59949950	Hela-S3	cervix:	n/a	n/a
6	TBP	chr15:59949309-59950002	K562	blood:	n/a	n/a
7	POLR2A	chr15:59949370-59950159	K562	blood:	n/a	n/a
8	POLR2A	chr15:59949323-59949991	Raji	blood:	n/a	n/a
9	POLR2A	chr15:59949349-59950011	GM12892	blood:	n/a	n/a
10	POLR2A	chr15:59949434-59949969	GM12892	blood:	n/a	n/a
11	MAZ	chr15:59949415-59950024	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:59949098-59950454	HepG2	liver:	n/a	n/a
13	RCOR1	chr15:59949533-59950065	GM12878	blood:	n/a	n/a
14	ELF1	chr15:59949406-59950157	A549	lung:	n/a	chr15:59950009-59950018 chr15:59949721-59949734 chr15:59950008-59950019 chr15:59949742-59949753
15	ELF1	chr15:59949131-59950049	GM12878	blood:	n/a	chr15:59950009-59950018 chr15:59949721-59949734 chr15:59950008-59950019 chr15:59949396-59949408 chr15:59949742-59949753
16	MXI1	chr15:59948690-59950336	SK-N-SH	brain:	n/a	n/a
17	EP300	chr15:59949600-59949899	K562	blood:	n/a	n/a
18	POLR2A	chr15:59949276-59950077	U87	brain:	n/a	n/a
19	SMARCB1	chr15:59949234-59950113	Hela-S3	cervix:	n/a	n/a
20	GABPA	chr15:59949359-59950001	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:59949278-59950069	GM19099	blood:	n/a	n/a
22	POLR2A	chr15:59949284-59950005	PBDE	blood:	n/a	n/a
23	POLR2A	chr15:59949166-59949897	Hela-S3	cervix:	n/a	n/a
24	SP1	chr15:59949569-59949959	GM12878	blood:	n/a	chr15:59949776-59949788 chr15:59949776-59949788 chr15:59949777-59949786 chr15:59949778-59949787
25	MXI1	chr15:59949539-59950048	H1-hESC	embryonic stem cell:	n/a	n/a
26	CBX3	chr15:59949520-59950387	K562	blood:	n/a	n/a
27	REST	chr15:59949316-59950012	A549	lung:	n/a	n/a
28	E2F6	chr15:59949299-59950103	A549	lung:	n/a	chr15:59949545-59949555
29	TAF1	chr15:59949287-59949905	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:59949328-59949966	MCF-7	breast:	n/a	n/a
31	PBX3	chr15:59949440-59950112	SK-N-SH	brain:	n/a	chr15:59949766-59949786
32	POLR2A	chr15:59949146-59950204	PFSK-1	brain:	n/a	n/a
33	ELF1	chr15:59949444-59949958	SK-N-SH	brain:	n/a	chr15:59949721-59949734 chr15:59949742-59949753
34	JUND	chr15:59949468-59949929	A549	lung:	n/a	chr15:59949542-59949551 chr15:59949543-59949552
35	TBP	chr15:59949471-59949907	HepG2	liver:	n/a	n/a
36	IRF1	chr15:59949476-59950076	K562	blood:	n/a	chr15:59949774-59949788
37	TAF1	chr15:59949401-59949952	MCF-7	breast:	n/a	n/a
38	POLR2A	chr15:59949330-59949952	Gliobla	brain:	n/a	n/a
39	SP4	chr15:59949509-59949984	H1-hESC	embryonic stem cell:	n/a	chr15:59949774-59949790
40	POLR2A	chr15:59949201-59950042	GM12891	blood:	n/a	n/a
41	POLR2A	chr15:59949141-59950170	SK-N-MC	brain:	n/a	n/a
42	POLR2A	chr15:59949447-59950010	K562	blood:	n/a	n/a
43	POLR2A	chr15:59949269-59949924	A549	lung:	n/a	n/a
44	HEY1	chr15:59949392-59949908	K562	blood:	n/a	chr15:59949445-59949460
45	POLR2A	chr15:59949445-59949947	GM12891	blood:	n/a	n/a
46	POLR2A	chr15:59949105-59950044	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr15:59949316-59949906	A549	lung:	n/a	n/a
48	FOXM1	chr15:59949281-59949952	GM12878	blood:	n/a	n/a
49	POLR2A	chr15:59949372-59949988	MCF-7	breast:	n/a	n/a
50	ELF1	chr15:59949406-59950040	MCF-7	breast:	n/a	chr15:59950009-59950018 chr15:59949721-59949734 chr15:59950008-59950019 chr15:59949742-59949753

No.	Distal block	Cell Line	Cell type
1	chr15:59680945..59682711-chr15:59948219..59950781,2	MCF-7	breast:
2	chr15:59949095..59949897-chr19:18668526..18669110,2	Hela-S3	cervix:
3	chr15:59948214..59950768-chr15:59963899..59966386,2	K562	blood:
4	chr15:59949368..59951651-chr15:60769964..60772749,2	K562	blood:
5	chr15:59947605..59950537-chr15:59979625..59981765,3	MCF-7	breast:
6	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
7	chr15:59949843..59951651-chr15:60768775..60771464,2	K562	blood:
8	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:

Variant related genes	Relation type
GTF2A2	TF binding region
ENSG00000238767	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000259238	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000227161	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1002181	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10152209	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10152373	0.86[YRI][hapmap]
rs10152414	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10152415	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10152509	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10152791	0.83[YRI][hapmap]
rs10162629	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1046053	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10519039	0.91[YRI][hapmap]
rs1057059	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071465	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071468	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11071469	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1135148	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs11634067	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637071	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11637359	0.91[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11853610	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11854063	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441240	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593480	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12708458	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12708459	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902582	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12902774	0.81[EUR][1000 genomes]
rs12903647	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12906392	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12907554	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907641	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12909005	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12910751	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12912652	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1479885	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1531638	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1531639	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552031	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16941648	0.95[YRI][hapmap]
rs17236804	0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1871499	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1871503	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1979422	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2101019	0.95[CEU][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2170062	0.82[EUR][1000 genomes]
rs2306355	0.88[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306357	0.95[JPT][hapmap];0.95[YRI][hapmap]
rs2307272	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2307273	0.95[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2307275	0.91[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes]
rs2414638	0.83[EUR][1000 genomes]
rs28671744	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2899649	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3087328	0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap]
rs34797071	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34894301	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784389	0.86[EUR][1000 genomes]
rs3825870	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs4232	0.82[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4270113	0.91[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4533213	0.94[EUR][1000 genomes]
rs4774340	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4774341	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4775191	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4775195	0.82[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775197	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151446	0.95[JPT][hapmap];0.95[YRI][hapmap]
rs6151447	0.95[JPT][hapmap];0.95[YRI][hapmap]
rs6151448	0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs6151449	0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs6151450	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6151458	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs6151459	0.88[EUR][1000 genomes]
rs6151460	0.94[EUR][1000 genomes]
rs6151461	0.91[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs6151462	0.90[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs6151467	0.94[EUR][1000 genomes]
rs6151470	0.94[EUR][1000 genomes]
rs6151472	0.93[EUR][1000 genomes]
rs6151474	0.94[EUR][1000 genomes]
rs6151477	0.94[EUR][1000 genomes]
rs6151483	0.91[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6151486	0.94[EUR][1000 genomes]
rs6151487	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6151496	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6151501	0.94[EUR][1000 genomes]
rs6151503	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151504	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151506	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6151510	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs6151514	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151525	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151528	0.95[EUR][1000 genomes]
rs6151529	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151532	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151533	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151535	0.86[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151536	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151542	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151545	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151551	0.91[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6151553	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6151557	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6151561	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151565	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151568	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151570	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151571	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151574	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151576	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6151580	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151581	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151586	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151588	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151589	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151590	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151592	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62012358	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62015260	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62015289	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494127	0.83[EUR][1000 genomes]
rs6494128	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6494130	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6494131	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494133	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67697180	0.87[EUR][1000 genomes]
rs67820349	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7162964	0.85[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7164756	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172270	0.83[EUR][1000 genomes]
rs7178050	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7180408	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182962	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs722163	0.94[EUR][1000 genomes]
rs722164	0.94[EUR][1000 genomes]
rs7497974	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs754642	0.94[JPT][hapmap]
rs7882	0.91[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8025415	0.95[YRI][hapmap]
rs8027679	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033161	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8040114	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8041394	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1871500	PRTG	cis	parietal	SCAN
rs1871500	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59947600-59950000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:59947600-59950200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr15:59947600-59950200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr15:59947600-59950400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:59947800-59950200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:59948200-59950000	Active TSS	HSMM	muscle
7	chr15:59948200-59950200	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr15:59948200-59950200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:59948400-59950000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:59948400-59950000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:59948400-59950000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:59948400-59950200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr15:59948400-59950200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:59948400-59950200	Active TSS	Fetal Kidney	kidney
15	chr15:59948400-59950400	Active TSS	Right Atrium	heart
16	chr15:59948600-59950000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:59948600-59950000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:59948600-59950000	Active TSS	Brain Angular Gyrus	brain
19	chr15:59948600-59950200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr15:59948600-59950200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:59948600-59950200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr15:59948600-59950200	Active TSS	Right Ventricle	heart
23	chr15:59948600-59950200	Active TSS	GM12878-XiMat	blood
24	chr15:59948600-59950200	Active TSS	HSMMtube	muscle
25	chr15:59948600-59950200	Active TSS	NHDF-Ad	bronchial
26	chr15:59948600-59950200	Active TSS	NHLF	lung
27	chr15:59948600-59950400	Active TSS	Fetal Intestine Large	intestine
28	chr15:59948600-59950400	Active TSS	Psoas Muscle	Psoas
29	chr15:59948600-59950600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr15:59948800-59950000	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr15:59948800-59950000	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr15:59948800-59950000	Active TSS	Small Intestine	intestine
33	chr15:59948800-59950000	Active TSS	HMEC	breast
34	chr15:59948800-59950200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:59948800-59950200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:59948800-59950200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:59948800-59950200	Active TSS	Aorta	Aorta
38	chr15:59948800-59950200	Active TSS	Fetal Intestine Small	intestine
39	chr15:59948800-59950200	Active TSS	Ovary	ovary
40	chr15:59948800-59950200	Active TSS	A549	lung
41	chr15:59948800-59950400	Active TSS	Brain Anterior Caudate	brain
42	chr15:59948800-59950400	Active TSS	Brain Germinal Matrix	brain
43	chr15:59948800-59950400	Active TSS	Brain Hippocampus Middle	brain
44	chr15:59949000-59950000	Active TSS	Primary T cells fromperipheralblood	blood
45	chr15:59949000-59950000	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr15:59949000-59950000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr15:59949000-59950000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr15:59949000-59950000	Active TSS	Fetal Brain Male	brain
49	chr15:59949000-59950000	Active TSS	Fetal Brain Female	brain
50	chr15:59949000-59950000	Active TSS	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links